Phosphorus in PDB 1agh: The Solution Structure of An 11 Base-Pair Oligonucleotide Duplex Coding For Amino Acids 60-62 of the Product of the N-Ras Protooncogene, uc(Nmr), Minimized Average Structure

Phosphorus Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Phosphorus atom in the The Solution Structure of An 11 Base-Pair Oligonucleotide Duplex Coding For Amino Acids 60-62 of the Product of the N-Ras Protooncogene, uc(Nmr), Minimized Average Structure (pdb code 1agh). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 20 binding sites of Phosphorus where determined in the The Solution Structure of An 11 Base-Pair Oligonucleotide Duplex Coding For Amino Acids 60-62 of the Product of the N-Ras Protooncogene, uc(Nmr), Minimized Average Structure, PDB code: 1agh:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 20 in 1agh

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Phosphorus binding site 1 out of 20 in the The Solution Structure of An 11 Base-Pair Oligonucleotide Duplex Coding For Amino Acids 60-62 of the Product of the N-Ras Protooncogene, uc(Nmr), Minimized Average Structure


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of The Solution Structure of An 11 Base-Pair Oligonucleotide Duplex Coding For Amino Acids 60-62 of the Product of the N-Ras Protooncogene, uc(Nmr), Minimized Average Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P2

b:1.3
occ:1.00
P A:DG2 0.0 1.3 1.0
OP1 A:DG2 1.5 1.5 1.0
OP2 A:DG2 1.5 2.3 1.0
O5' A:DG2 1.6 1.2 1.0
O3' A:DC1 1.6 1.2 1.0
H2'' A:DC1 2.5 1.0 1.0
C5' A:DG2 2.7 1.2 1.0
C3' A:DC1 2.7 1.2 1.0
H5'' A:DG2 2.8 1.3 1.0
H5' A:DG2 2.9 1.2 1.0
H3' A:DC1 3.1 1.3 1.0
C2' A:DC1 3.1 1.0 1.0
H8 A:DG2 3.6 0.9 1.0
H2' A:DC1 3.8 1.0 1.0
H3' A:DG2 3.9 1.3 1.0
C4' A:DG2 4.0 1.1 1.0
C4' A:DC1 4.0 1.2 1.0
H4' A:DC1 4.0 1.3 1.0
H2' A:DG2 4.1 1.1 1.0
H1' A:DC1 4.2 0.9 1.0
C1' A:DC1 4.2 1.0 1.0
C3' A:DG2 4.4 1.1 1.0
O4' A:DG2 4.5 0.9 1.0
C8 A:DG2 4.6 0.8 1.0
O4' A:DC1 4.7 1.1 1.0
C2' A:DG2 4.7 1.0 1.0
H4' A:DG2 4.8 1.1 1.0

Phosphorus binding site 2 out of 20 in 1agh

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Phosphorus binding site 2 out of 20 in the The Solution Structure of An 11 Base-Pair Oligonucleotide Duplex Coding For Amino Acids 60-62 of the Product of the N-Ras Protooncogene, uc(Nmr), Minimized Average Structure


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of The Solution Structure of An 11 Base-Pair Oligonucleotide Duplex Coding For Amino Acids 60-62 of the Product of the N-Ras Protooncogene, uc(Nmr), Minimized Average Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:1.3
occ:1.00
P A:DG3 0.0 1.3 1.0
OP2 A:DG3 1.4 2.3 1.0
OP1 A:DG3 1.4 1.8 1.0
O5' A:DG3 1.5 1.2 1.0
O3' A:DG2 1.6 1.3 1.0
C5' A:DG3 2.5 1.2 1.0
C3' A:DG2 2.6 1.1 1.0
H5'' A:DG3 2.6 1.3 1.0
H2'' A:DG2 2.6 1.1 1.0
H5' A:DG3 2.8 1.2 1.0
H3' A:DG2 2.8 1.3 1.0
C2' A:DG2 3.1 1.0 1.0
H3' A:DG3 3.5 1.2 1.0
H2' A:DG2 3.7 1.1 1.0
C4' A:DG3 3.8 1.0 1.0
C4' A:DG2 3.9 1.1 1.0
H8 A:DG3 3.9 0.9 1.0
H4' A:DG2 4.0 1.1 1.0
H1' A:DG2 4.1 0.9 1.0
C3' A:DG3 4.1 1.0 1.0
C1' A:DG2 4.1 0.9 1.0
H2' A:DG3 4.3 1.0 1.0
O4' A:DG3 4.5 0.9 1.0
H4' A:DG3 4.5 1.0 1.0
O4' A:DG2 4.6 0.9 1.0
C2' A:DG3 4.7 0.9 1.0
H5'' A:DG2 4.8 1.3 1.0
C5' A:DG2 4.9 1.2 1.0
C8 A:DG3 4.9 0.8 1.0

Phosphorus binding site 3 out of 20 in 1agh

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Phosphorus binding site 3 out of 20 in the The Solution Structure of An 11 Base-Pair Oligonucleotide Duplex Coding For Amino Acids 60-62 of the Product of the N-Ras Protooncogene, uc(Nmr), Minimized Average Structure


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of The Solution Structure of An 11 Base-Pair Oligonucleotide Duplex Coding For Amino Acids 60-62 of the Product of the N-Ras Protooncogene, uc(Nmr), Minimized Average Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:1.1
occ:1.00
P A:DA4 0.0 1.1 1.0
OP2 A:DA4 1.5 1.8 1.0
OP1 A:DA4 1.5 1.7 1.0
O5' A:DA4 1.6 0.9 1.0
O3' A:DG3 1.6 1.0 1.0
H2'' A:DG3 2.5 0.9 1.0
C5' A:DA4 2.6 0.9 1.0
C3' A:DG3 2.6 1.0 1.0
H5'' A:DA4 2.8 1.0 1.0
H5' A:DA4 2.9 0.9 1.0
H3' A:DG3 3.0 1.2 1.0
C2' A:DG3 3.0 0.9 1.0
H8 A:DA4 3.5 0.9 1.0
H2' A:DG3 3.7 1.0 1.0
H3' A:DA4 3.9 0.9 1.0
C4' A:DG3 3.9 1.0 1.0
C4' A:DA4 4.0 0.9 1.0
H4' A:DG3 4.0 1.0 1.0
H1' A:DG3 4.1 0.8 1.0
C1' A:DG3 4.2 0.8 1.0
C3' A:DA4 4.4 0.9 1.0
O4' A:DA4 4.4 0.9 1.0
C8 A:DA4 4.5 0.8 1.0
O4' A:DG3 4.6 0.9 1.0
H2' A:DA4 4.7 0.8 1.0
H4' A:DA4 4.8 0.9 1.0
H5'' A:DG3 4.8 1.3 1.0
C5' A:DG3 5.0 1.2 1.0

Phosphorus binding site 4 out of 20 in 1agh

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Phosphorus binding site 4 out of 20 in the The Solution Structure of An 11 Base-Pair Oligonucleotide Duplex Coding For Amino Acids 60-62 of the Product of the N-Ras Protooncogene, uc(Nmr), Minimized Average Structure


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of The Solution Structure of An 11 Base-Pair Oligonucleotide Duplex Coding For Amino Acids 60-62 of the Product of the N-Ras Protooncogene, uc(Nmr), Minimized Average Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P5

b:1.0
occ:1.00
P A:DC5 0.0 1.0 1.0
OP1 A:DC5 1.5 1.7 1.0
OP2 A:DC5 1.5 1.6 1.0
O3' A:DA4 1.6 1.0 1.0
O5' A:DC5 1.6 1.0 1.0
H2'' A:DA4 2.6 0.9 1.0
C5' A:DC5 2.7 1.0 1.0
C3' A:DA4 2.7 0.9 1.0
H5' A:DC5 2.9 1.1 1.0
H5'' A:DC5 2.9 1.1 1.0
H3' A:DA4 3.0 0.9 1.0
C2' A:DA4 3.1 0.9 1.0
H6 A:DC5 3.7 0.8 1.0
H2' A:DA4 3.7 0.8 1.0
H3' A:DC5 3.9 0.9 1.0
C4' A:DA4 4.0 0.9 1.0
C4' A:DC5 4.0 0.9 1.0
H4' A:DA4 4.0 0.9 1.0
C1' A:DA4 4.3 0.8 1.0
H1' A:DA4 4.4 0.9 1.0
O4' A:DC5 4.4 0.9 1.0
C3' A:DC5 4.5 0.9 1.0
C6 A:DC5 4.7 0.7 1.0
H2' A:DC5 4.7 0.8 1.0
O4' A:DA4 4.7 0.9 1.0
H4' A:DC5 4.8 1.0 1.0
H5'' A:DA4 4.9 1.0 1.0

Phosphorus binding site 5 out of 20 in 1agh

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Phosphorus binding site 5 out of 20 in the The Solution Structure of An 11 Base-Pair Oligonucleotide Duplex Coding For Amino Acids 60-62 of the Product of the N-Ras Protooncogene, uc(Nmr), Minimized Average Structure


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of The Solution Structure of An 11 Base-Pair Oligonucleotide Duplex Coding For Amino Acids 60-62 of the Product of the N-Ras Protooncogene, uc(Nmr), Minimized Average Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P6

b:0.9
occ:1.00
P A:DA6 0.0 0.9 1.0
OP2 A:DA6 1.5 1.7 1.0
OP1 A:DA6 1.5 1.5 1.0
O5' A:DA6 1.6 0.9 1.0
O3' A:DC5 1.6 1.0 1.0
C5' A:DA6 2.6 0.9 1.0
H2'' A:DC5 2.6 0.8 1.0
C3' A:DC5 2.6 0.9 1.0
H5'' A:DA6 2.7 1.0 1.0
H3' A:DC5 2.9 0.9 1.0
H5' A:DA6 3.0 0.9 1.0
C2' A:DC5 3.1 0.8 1.0
H8 A:DA6 3.3 0.7 1.0
H3' A:DA6 3.7 0.8 1.0
H2' A:DC5 3.7 0.8 1.0
C4' A:DA6 3.9 0.8 1.0
C4' A:DC5 4.0 0.9 1.0
H4' A:DC5 4.0 1.0 1.0
H2' A:DA6 4.3 0.7 1.0
C3' A:DA6 4.3 0.8 1.0
C1' A:DC5 4.3 0.8 1.0
C8 A:DA6 4.3 0.6 1.0
H1' A:DC5 4.3 0.8 1.0
O4' A:DA6 4.5 0.7 1.0
H4' A:DA6 4.7 0.9 1.0
C2' A:DA6 4.7 0.7 1.0
O4' A:DC5 4.8 0.9 1.0
H5'' A:DC5 4.8 1.1 1.0
C5' A:DC5 5.0 1.0 1.0

Phosphorus binding site 6 out of 20 in 1agh

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Phosphorus binding site 6 out of 20 in the The Solution Structure of An 11 Base-Pair Oligonucleotide Duplex Coding For Amino Acids 60-62 of the Product of the N-Ras Protooncogene, uc(Nmr), Minimized Average Structure


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of The Solution Structure of An 11 Base-Pair Oligonucleotide Duplex Coding For Amino Acids 60-62 of the Product of the N-Ras Protooncogene, uc(Nmr), Minimized Average Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P7

b:0.9
occ:1.00
P A:DA7 0.0 0.9 1.0
OP1 A:DA7 1.5 1.7 1.0
OP2 A:DA7 1.5 1.5 1.0
O3' A:DA6 1.6 0.8 1.0
O5' A:DA7 1.6 0.8 1.0
H2'' A:DA6 2.6 0.7 1.0
C3' A:DA6 2.7 0.8 1.0
C5' A:DA7 2.7 1.0 1.0
H5'' A:DA7 2.9 1.3 1.0
H5' A:DA7 2.9 1.2 1.0
H3' A:DA6 3.0 0.8 1.0
C2' A:DA6 3.1 0.7 1.0
H8 A:DA7 3.7 0.7 1.0
H2' A:DA6 3.8 0.7 1.0
C4' A:DA6 4.0 0.8 1.0
H3' A:DA7 4.0 0.9 1.0
C4' A:DA7 4.0 0.9 1.0
H4' A:DA6 4.0 0.9 1.0
C1' A:DA6 4.3 0.6 1.0
H1' A:DA6 4.3 0.6 1.0
H2' A:DA7 4.4 0.8 1.0
O4' A:DA7 4.4 0.8 1.0
C3' A:DA7 4.5 0.9 1.0
C8 A:DA7 4.6 0.6 1.0
O4' A:DA6 4.7 0.7 1.0
H4' A:DA7 4.8 1.0 1.0
C2' A:DA7 4.9 0.8 1.0
H5'' A:DA6 5.0 1.0 1.0

Phosphorus binding site 7 out of 20 in 1agh

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Phosphorus binding site 7 out of 20 in the The Solution Structure of An 11 Base-Pair Oligonucleotide Duplex Coding For Amino Acids 60-62 of the Product of the N-Ras Protooncogene, uc(Nmr), Minimized Average Structure


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of The Solution Structure of An 11 Base-Pair Oligonucleotide Duplex Coding For Amino Acids 60-62 of the Product of the N-Ras Protooncogene, uc(Nmr), Minimized Average Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P8

b:1.2
occ:1.00
P A:DG8 0.0 1.2 1.0
OP1 A:DG8 1.5 1.7 1.0
OP2 A:DG8 1.5 2.2 1.0
O5' A:DG8 1.6 1.0 1.0
O3' A:DA7 1.6 0.9 1.0
H2'' A:DA7 2.6 0.8 1.0
C5' A:DG8 2.7 1.0 1.0
C3' A:DA7 2.7 0.9 1.0
H5'' A:DG8 2.8 1.1 1.0
H5' A:DG8 3.0 1.1 1.0
H3' A:DA7 3.0 0.9 1.0
C2' A:DA7 3.1 0.8 1.0
H8 A:DG8 3.7 0.6 1.0
H2' A:DA7 3.8 0.8 1.0
H3' A:DG8 3.9 0.8 1.0
C4' A:DG8 4.0 0.8 1.0
C4' A:DA7 4.0 0.9 1.0
H4' A:DA7 4.0 1.0 1.0
H1' A:DA7 4.1 0.7 1.0
H2' A:DG8 4.2 0.7 1.0
C1' A:DA7 4.2 0.7 1.0
C3' A:DG8 4.4 0.7 1.0
O4' A:DG8 4.5 0.7 1.0
C8 A:DG8 4.7 0.6 1.0
O4' A:DA7 4.7 0.8 1.0
C2' A:DG8 4.8 0.6 1.0
H4' A:DG8 4.8 0.9 1.0

Phosphorus binding site 8 out of 20 in 1agh

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Phosphorus binding site 8 out of 20 in the The Solution Structure of An 11 Base-Pair Oligonucleotide Duplex Coding For Amino Acids 60-62 of the Product of the N-Ras Protooncogene, uc(Nmr), Minimized Average Structure


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of The Solution Structure of An 11 Base-Pair Oligonucleotide Duplex Coding For Amino Acids 60-62 of the Product of the N-Ras Protooncogene, uc(Nmr), Minimized Average Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P9

b:0.7
occ:1.00
P A:DA9 0.0 0.7 1.0
OP2 A:DA9 1.5 1.2 1.0
OP1 A:DA9 1.5 1.7 1.0
O3' A:DG8 1.6 0.7 1.0
O5' A:DA9 1.6 0.6 1.0
H5'' A:DA9 2.6 0.8 1.0
C5' A:DA9 2.6 0.7 1.0
C3' A:DG8 2.7 0.7 1.0
H2'' A:DG8 2.9 0.6 1.0
H3' A:DG8 2.9 0.8 1.0
H5' A:DA9 3.2 0.7 1.0
C2' A:DG8 3.3 0.6 1.0
H8 A:DA9 3.4 0.5 1.0
H3' A:DA9 3.5 0.7 1.0
C4' A:DA9 3.9 0.7 1.0
C4' A:DG8 3.9 0.8 1.0
H4' A:DG8 4.0 0.9 1.0
H2' A:DG8 4.0 0.7 1.0
C3' A:DA9 4.2 0.7 1.0
H1' A:DG8 4.3 0.6 1.0
C8 A:DA9 4.3 0.4 1.0
C1' A:DG8 4.4 0.6 1.0
H2' A:DA9 4.4 0.6 1.0
O4' A:DA9 4.4 0.6 1.0
H4' A:DA9 4.7 0.7 1.0
O4' A:DG8 4.7 0.7 1.0
C2' A:DA9 4.8 0.6 1.0
H5'' A:DG8 4.8 1.1 1.0
C5' A:DG8 5.0 1.0 1.0

Phosphorus binding site 9 out of 20 in 1agh

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Phosphorus binding site 9 out of 20 in the The Solution Structure of An 11 Base-Pair Oligonucleotide Duplex Coding For Amino Acids 60-62 of the Product of the N-Ras Protooncogene, uc(Nmr), Minimized Average Structure


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of The Solution Structure of An 11 Base-Pair Oligonucleotide Duplex Coding For Amino Acids 60-62 of the Product of the N-Ras Protooncogene, uc(Nmr), Minimized Average Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P10

b:1.1
occ:1.00
P A:DA10 0.0 1.1 1.0
OP1 A:DA10 1.5 1.4 1.0
OP2 A:DA10 1.5 2.2 1.0
O5' A:DA10 1.6 0.9 1.0
O3' A:DA9 1.6 0.8 1.0
H2'' A:DA9 2.6 0.6 1.0
C5' A:DA10 2.7 1.0 1.0
C3' A:DA9 2.7 0.7 1.0
H5'' A:DA10 2.8 1.1 1.0
H5' A:DA10 3.0 1.0 1.0
H3' A:DA9 3.0 0.7 1.0
C2' A:DA9 3.1 0.6 1.0
H2' A:DA9 3.7 0.6 1.0
H3' A:DA10 3.7 1.0 1.0
C4' A:DA9 4.0 0.7 1.0
C4' A:DA10 4.0 0.9 1.0
H4' A:DA9 4.0 0.7 1.0
H8 A:DA10 4.0 0.6 1.0
C1' A:DA9 4.3 0.5 1.0
C3' A:DA10 4.4 0.9 1.0
H1' A:DA9 4.4 0.6 1.0
O4' A:DA10 4.5 0.8 1.0
H2' A:DA10 4.6 0.8 1.0
O4' A:DA9 4.7 0.6 1.0
H4' A:DA10 4.8 1.0 1.0
H5'' A:DA9 4.8 0.8 1.0
C8 A:DA10 4.9 0.6 1.0
C2' A:DA10 5.0 0.8 1.0

Phosphorus binding site 10 out of 20 in 1agh

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Phosphorus binding site 10 out of 20 in the The Solution Structure of An 11 Base-Pair Oligonucleotide Duplex Coding For Amino Acids 60-62 of the Product of the N-Ras Protooncogene, uc(Nmr), Minimized Average Structure


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of The Solution Structure of An 11 Base-Pair Oligonucleotide Duplex Coding For Amino Acids 60-62 of the Product of the N-Ras Protooncogene, uc(Nmr), Minimized Average Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P11

b:1.4
occ:1.00
P A:DG11 0.0 1.4 1.0
OP1 A:DG11 1.5 2.1 1.0
OP2 A:DG11 1.5 2.3 1.0
O5' A:DG11 1.6 1.3 1.0
O3' A:DA10 1.6 1.0 1.0
C5' A:DG11 2.6 1.5 1.0
H2'' A:DA10 2.7 0.9 1.0
C3' A:DA10 2.7 0.9 1.0
H5'' A:DG11 2.7 1.4 1.0
H3' A:DA10 2.9 1.0 1.0
H5' A:DG11 3.0 1.8 1.0
C2' A:DA10 3.1 0.8 1.0
H8 A:DG11 3.2 1.2 1.0
H3' A:DG11 3.5 1.8 1.0
H2' A:DA10 3.7 0.8 1.0
C4' A:DG11 3.9 1.6 1.0
C4' A:DA10 4.0 0.9 1.0
H4' A:DA10 4.0 1.0 1.0
C3' A:DG11 4.2 1.7 1.0
C8 A:DG11 4.2 1.1 1.0
C1' A:DA10 4.3 0.7 1.0
H1' A:DA10 4.4 0.8 1.0
O4' A:DG11 4.6 1.5 1.0
H2' A:DG11 4.6 1.6 1.0
H4' A:DG11 4.7 1.7 1.0
O4' A:DA10 4.8 0.8 1.0
H5'' A:DA10 4.9 1.1 1.0
C2' A:DG11 4.9 1.6 1.0
C5' A:DA10 5.0 1.0 1.0
N7 A:DG11 5.0 1.0 1.0

Reference:

B.Feng, M.P.Stone. Solution Structure of An Oligodeoxynucleotide Containing the Human N-Ras Codon 61 Sequence Refined From 1H uc(Nmr) Using Molecular Dynamics Restrained By Nuclear Overhauser Effects. Chem.Res.Toxicol. V. 8 821 1995.
ISSN: ISSN 0893-228X
PubMed: 7492731
DOI: 10.1021/TX00048A002
Page generated: Fri Sep 25 12:51:08 2020

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